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1,298 results for “Archive”
christofs/berardier: First full archive of berardier.org
<p>This is an archival copy of all content on berardier.org.</p>
Data Archive for "Speckle Noise Reduction via Linewidth Broadening for Planetary Laser Reflectance Spectrometers"
<p>This archive contains the raw speckle images and experimental notes for the data contained in the journal article: "Speckle Noise Reduction via Linewidth Broadening for Planetary Laser Reflectance Spectrometers".</p> <p>The data available are:</p> <p>Raw speckle images for each of 5 illumination sources:</p> <ol> <li>Single-Frequence diode (files are named "IPS")</li> <li>Dual Mode pump diode (files are named "II-IV")</li> <li>Fabry Perot didoe (files are names "FP")</li> <li>Superluminescent Diode (files are named "SLD")</li> <li>Whilte light halogen source (files are named "WL")</li> </ol> <p>For each of theses source there are 5 images for each reflectance target, four speckle patterns and one background image with the laser source off. The naming convention is:</p> <p>LaserName_TargetReflectance_Target Rotation State or BKG.tiff</p> <p>For example, IPS_50_2 is the single-frequency laser using the 50% reflectance target and second rotation state of the target.</p> <p>The integration time for each image is give in the file "Experiment Paramters.csv" and was manually change to keep the maximum intensity at roughly 75% saturation.</p> <p>The spectra of the three laser sources presented in the manuscript are also included as .csv files</p>
Replication Archive for "Teen Social Interactions and Well-being during the COVID-19 Pandemic"
<p><span>This archive includes the Stata code to replicate all results in the referenced paper.</span></p>
Source Code Archiving to the Rescue of Reproducible Deployment — Replication Package
<p>Replication package for the paper:</p> <p>Ludovic Courtès, Timothy Sample, Simon Tournier, Stefano Zacchiroli.<br><em>Source Code Archiving to the Rescue of Reproducible Deployment</em><br><a href="https://acm-rep.github.io/2024/">ACM REP'24</a>, June 18-20, 2024, Rennes, France<br><a href="https://doi.org/10.1145/3641525.3663622">https://doi.org/10.1145/3641525.3663622</a></p> <h2>Generating the paper</h2> <p>The paper can be generated using the following command:</p> <pre><code>guix time-machine -C channels.scm \ -- shell -C -m manifest.scm \ -- make </code></pre> <p>This uses GNU Guix to run <code>make</code> in the exact same computational environment used when preparing the paper. The computational environment is described by two files. The <code>channels.scm</code> file specifies the exact version of the Guix package collection to use. The <code>manifest.scm</code> file selects a subset of those packages to include in the environment.</p> <p>It may be possible to generate the paper without Guix. To do so, you will need the following software (on top of a Unix-like environment):</p> <ul> <li>GNU Make</li> <li>SQLite 3</li> <li>GNU AWK</li> <li>Rubber</li> <li>Graphviz</li> <li>TeXLive</li> </ul> <h2>Structure</h2> <ul> <li><code>data/</code> contains the data examined in the paper</li> <li><code>scripts/</code> contains dedicated code for the paper</li> <li><code>logs/</code> contains logs generated during certain computations</li> </ul> <h2>Preservation of Guix</h2> <p>Some of the claims in the paper come from analyzing the Preservation of Guix (PoG) database as published on January 26, 2024. This database is the result of years of monitoring the extent to which the source code referenced by Guix packages is archived. This monitoring has been carried out by Timothy Sample who occasionally publishes reports on his personal website: <a href="https://ngyro.com/pog-reports/latest/">https://ngyro.com/pog-reports/latest/</a>. The database included in this package (<code>data/pog.sql</code>) was downloaded from <a href="https://ngyro.com/pog-reports/2024-01-26/pog.db">https://ngyro.com/pog-reports/2024-01-26/pog.db</a> and then exported to SQL format. In addition to the SQL file, the database schema is also included in this package as <code>data/schema.sql</code>.</p> <p>The database itself is largely the result of scripts, but also of manual adjustments (where necessary or convenient). The scripts are available at <a href="https://git.ngyro.com/preservation-of-guix/">https://git.ngyro.com/preservation-of-guix/</a>, which is preserved in the Software Heritage archive as well: <a href="https://archive.softwareheritage.org/swh:1:snp:efba3456a4aff0bc25b271e128aa8340ae2bc816;origin=https://git.ngyro.com/preservation-of-guix">https://archive.softwareheritage.org/swh:1:snp:efba3456a4aff0bc25b271e128aa8340ae2bc816;origin=https://git.ngyro.com/preservation-of-guix</a>. These scripts rely on the availability of source code in certain locations on the Internet, and therefore will not yield exactly the same result when run again.</p> <h3>Analysis</h3> <p>Here is an overview of how we use the PoG database in the paper. The exact way it is queried to produce graphs and tables for the paper is laid out in the Makefile.</p> <p>The <code>pog-types.sql</code> query gives the counts of each source type (e.g. “git” or “tar-gz”) for each commit covered by the database.</p> <p>The <code>pog-status.sql</code> query gives the archival status of the sources by commit. For each commit, it produces a count of how many sources are <em>stored</em> in the Software Heritage archive, <em>missing</em> from it, or <em>unknown</em> if stored or missing. The <code>pog-status-total.sql</code> query does the same thing but over all sources without sorting them into individual commits.</p> <p>The <code>disarchive-ratio.sql</code> query estimates the success rate of Disarchive disassembly.</p> <p>Finally, the <code>swhid-ratio.sql</code> query gives the proportion of sources for which the PoG database has an SWHID.</p> <h3>Estimating missing sources</h3> <p>The Preservation of Guix database only covers sources from a sample of commits to the Guix repository. This greatly simplifies the process of collecting the sources at the risk of missing a few. We estimate how many are missed by searching Guix’s Git history for Nix-style base-32 hashes. The result of this search is compared to the hashes in the PoG database.</p> <p>A naïve search of Git history results in an over estimate due to Guix’s branch development model. We find hashes that were never exposed to users of ‘guix pull’. To work around this, we also approximate the history of commits available to ‘guix pull’. We do this by scraping push events from the guix-commits mailing list archives (<code>data/guix-commits.mbox</code>). Unfortunately, those archives are not quite complete. Missing history is reconstructed in the <code>data/missing-links.txt</code> file.</p> <p>This estimate requires a copy of the Guix Git repository (not included in this package). The repository can be obtained from GNU at <a href="https://git.savannah.gnu.org/git/guix.git">https://git.savannah.gnu.org/git/guix.git</a> or from the Software Heritage archive: <a href="https://archive.softwareheritage.org/swh:1:snp:9d7b8dcf5625c17e42d51357848baa226b70e4bb;origin=https://git.savannah.gnu.org/git/guix.git">https://archive.softwareheritage.org/swh:1:snp:9d7b8dcf5625c17e42d51357848baa226b70e4bb;origin=https://git.savannah.gnu.org/git/guix.git</a>. Once obtained, its location must be specified in the Makefile.</p> <p>To generate the estimate, use:</p> <pre><code>guix time-machine -C channels.scm \ -- shell -C -m manifest.scm \ -- make data/missing-sources.txt </code></pre> <p>If not using Guix, you will need additional software beyond what is used to generate the paper:</p> <ul> <li>GNU Guile</li> <li>GNU Bash</li> <li>GNU Mailutils</li> <li>GNU Parallel</li> </ul> <h2>Measuring link rot</h2> <p>In order to measure link rot, we ran Guix Scheme scripts, i.e., scripts that exploit Guix as a Scheme library. The scripts depend on the state of world at the very specific moment when they ran. Hence, it is not possible to reproduce the exact same outputs. However, their tendency over the passing of time should be very similar. For running them, you need an installation of <a href="https://guix.gnu.org/manual/deve/en/html_node/Installation.html">Guix</a>. For instance,</p> <pre><code>guix repl -q scripts/table-per-origin.scm </code></pre> <p>When running these scripts for the paper, we tracked their output and saved it inside the <code>logs</code> directory.</p>
Рис. 8. A – Директор Зоологического института академик Е.Н. Павловский и Зам. директора института О.А. Скарлато в кабинете директора ЗИНа. 1963 г. Архив С.О. Скарлато; B – Директор Зоологического института член-корр. АН СССР О.А. Скарлато в кабинете директора ЗИНа. НоЯбрь 1990 г. Архив С.О. Скарлато. Fig. 8. A – Director of the Zoological Institute, Academician E.N. Pavlovsky and Deputy Director of the Institute O.A. Scarlato in the Director's Office. 1963. Archive of S.O. Scarlato; B – Director of the Zoological Institute, Corresponding Member O.A. Scarlato in the Director's Office. November 1990. Archive of S.O. Scarlato. in Orest A. Scarlato - scientist and organizer of science: on the 100th anniversary of his birth (1920-1994)
Рис. 8. A – Директор Зоологического института академик Е.Н. Павловский и Зам. директора института О.А. Скарлато в кабинете директора ЗИНа. 1963 г. Архив С.О. Скарлато; B – Директор Зоологического института член-корр. АН СССР О.А. Скарлато в кабинете директора ЗИНа. НоЯбрь 1990 г. Архив С.О. Скарлато. Fig. 8. A – Director of the Zoological Institute, Academician E.N. Pavlovsky and Deputy Director of the Institute O.A. Scarlato in the Director's Office. 1963. Archive of S.O. Scarlato; B – Director of the Zoological Institute, Corresponding Member O.A. Scarlato in the Director's Office. November 1990. Archive of S.O. Scarlato.
Reading Journal of eScience Librarianship: Responsible AI in Libraries and Archives
A special issue of Journal of eScience Librarianship was brought to my attention. The issue was on the topic of responsible AI in libraries and archives. I did a bit of distant reading against the issue, and outlined here are some of my take-aways. In short, AI is something to consider in Library Land, but not without some forethought.
Dataset of KO journal paper: Semantic analysis of archival concepts in CIDOC-CRM and in RiC-CM and RiC-O
<p>Semantic analysis of archival concepts (class, relations, atributtes, and relation attributes) presents in Records in Context family (conceptual model and ontology) and its possible equivalents in CIDOC-CRM.</p>
Fig. 6 in Archive reports and memories. The Brera Botanical Garden of Milan (1982-2001)
Fig. 6 - The Garden today. / L'Orto oggi. (Courtesy Università degli Studi di Milano - MOBE, Museo Orto Botanico di Brera ed Erbario).
Fig. 5 in Archive reports and memories. The Brera Botanical Garden of Milan (1982-2001)
Fig. 5 - Poster of the Northern Park showing the activity carried out with the Botanical Garden in 1999. / Poster del Parco Nord con l'indicazione dell'attività svolta con l'Orto nel 1999. (Courtesy Università degli Studi di Milano - MOBE, Museo Orto Botanico di Brera ed Erbario).
Fig. 4 - The school adopts a in Archive reports and memories. The Brera Botanical Garden of Milan (1982-2001)
Fig. 4 - The school adopts a monument, activity carried out by the Garden and the Parini School in the school years 1996-1997 and 1997-1998. / La scuola adotta un monumento, attività coordinata dall'Orto e dalla Scuola Media Parini negli anni scolastici 1996-1997 e 1997-1998. (Courtesy Università degli Studi di Milano - MOBE, Museo Orto Botanico di Brera ed Erbario).
Fig. 3 in Archive reports and memories. The Brera Botanical Garden of Milan (1982-2001)
Fig. 3 - Layout of the Project La Pietra & Magistretti (1989). / Pianta del Progetto La Pietra & Magistretti (1989). (Courtesy Università degli Studi di Milano - MOBE, Museo Orto Botanico di Brera ed Erbario).
Fig. 1 in Archive reports and memories. The Brera Botanical Garden of Milan (1982-2001)
Fig. 1 - The part of the Historical Archive of the Brera Botanical Garden ordered so far (1982-2001). / La parte dell'Archivio storico dell'Orto Botanico di Brera ad oggi ordinata (1982-2001). (Courtesy Università degli Studi di Milano - MOBE, Museo Orto Botanico di Brera ed Erbario).
Fig. 2 in Archive reports and memories. The Brera Botanical Garden of Milan (1982-2001)
Fig. 2 - The Garden's state of neglect in the 1980s. / Lo stato di abbandono dell'Orto negli anni Ottanta. (Courtesy Università degli Studi di Milano - MOBE, Museo Orto Botanico di Brera ed Erbario).
Linked collectors and determiners for: NEON Biorepository Invertebrate Bycatch Collection (Archive Pooling).
Natural history specimen data linked to collectors and determiners held within, "NEON Biorepository Invertebrate Bycatch Collection (Archive Pooling)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="http://bionomia.net/dataset/596bde6d-0df5-46cb-8eef-92dc3f169ceb">https://bionomia.net/dataset/596bde6d-0df5-46cb-8eef-92dc3f169ceb</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/596bde6d-0df5-46cb-8eef-92dc3f169ceb">https://gbif.org/dataset/596bde6d-0df5-46cb-8eef-92dc3f169ceb</a>. Formatted as a Frictionless Data package.
Data archive: Niche overlap between a cold-water coral and an associated sponge for isotopically-enriched particulate food sources
<p>Data belonging to the paper: </p> <p>Dick van Oevelen, Christina E. Mueller, Tomas Lundälv, Fleur C. van Duyl, Jasper M. de Goeij, Jack J. Middelburg<span> </span>(In press) <strong>Niche overlap between a cold-water coral and an associated sponge for isotopically-enriched particulate food sources</strong>. PLOS ONE</p>
FEED Archive
<p>The Feeding Experiments End-User Database (FEED) was designed by the <a href="http://nescent.org/science/awards_summary.php?id=150">Mammalian Feeding Apparatus Working Group</a> supported by the <a href="http://www.nescent.org/">National Evolutionary Synthesis Center (NESCent)</a>. See Additional Notes for information on (1) accessing the source code for the FEEDv2.0.3 database, and (2) accessing the ontologies (MFMO and OPBO).</p> <p>The data are archived here. The raw data are in .dat files, and the metadata pertaining to a specific numbered trial are in .csv format. All raw data and metadata are available for re-use. The .csv files named with the convention "trial_####_channels" contain metadata pertaining to an individual trial. The complete list of trials available for download, including relevant metadata for analyzing the in vivo data, are in the file "FEED_Archive_Master_Trials.csv". Raw data and metadata uploaded here are from FEEDv2 (2008-2018).</p> <p>FEED design and development funded by NSF-ABI-1062333 (CEW) and NSF-EF-0423641. NSF-EF0423641 funded the National Evolution Synthesis Center (NESCent) at Duke University (Principal Investigator: K. K. Smith).</p> <p>PUBLICATIONS AND HOW TO CITE:</p> <p>If you use the FEED data, ontologies, or application, or publish results attained from it, please cite as follows:<br> Wall, C. E., Vinyard, C. J., Williams, S. H., Gapeyev, V., Liu, X., Lapp, H., and German, R. Z. 2011. Overview of FEED, the Feeding Experiments End-User Database. Integrative and Comparative Biology 51(2):215-223. <a href="http://dx.doi.org/10.1093/icb/icr047">http://dx.doi.org/10.1093/icb/icr047</a>.</p> <p>Analysis of the raw EMGs in this FEED Archive can be analyzed with tools developed by Ying and Wall (2016). Please cite as follows:</p> <p>Ying, R. and Wall, C. E. (2016) A method for discrimination of noise and EMG signal regions recorded during rhythmic behaviors. Journal of Biomechanics 49:4113-4118. http://dx.doi.org/10.1016/j.jbiomech.2016.10.010. The tools are in a set of MATLAB (The Mathworks, Inc.) code is available for download at Github (https://github.com/FEEDEXP/EMG-Extractor). </p>
Data archive for Allen and Nettle, 'Hunger and socioeconomic background additively predict impulsivity in humans'
<p>This archive contains the raw data from Allen and Nettle, 'Hunger and socioeconomic background additively predict impulsivity in humans', plus R code for the data analyses. The impulsivity measure (HMDT) used in studies 2 and 3 is also included here. </p> <p>The R script 'IndividualAnalysis.R' performs the analysis of each study individually. 'MetaAnalysis.R' performs the meta-analysis. The three .csv files are the raw data from the three studies respectively. </p>
agitter/single-cell-pseudotime: 2018-06-25 archive
<p>An overview of algorithms for estimating pseudotime in single-cell RNA-seq data. Initial archive for Zenodo DOI and citation. Adopting release practices from <a href="https://github.com/seandavi/awesome-single-cell">https://github.com/seandavi/awesome-single-cell</a>.</p> <p>Thank you Jeff Hammerbacher for the corrections in this release.</p> <p>See <a href="https://github.com/agitter/single-cell-pseudotime">https://github.com/agitter/single-cell-pseudotime</a> for the latest version.</p> <ul> </ul>
PLD results with Archives of the Old University of Leuven: 22
<p>Combination of screenshots with 'color' and 'sketch1' shader of Archives of the Old University of Leuven: 22 (KU Leuven University Archives), i.e. the front of the pendant seal of Emperor Charles V, rendered in PLDviewer 7.0.05.</p>
Data archive for Gott et al. 'Chronological age, biological age, and individual variation in the stress response in the European starling: A follow-up study'
<p>Data archive for Gott et al. 'Chronological age, biological age, and individual variation in the stress response in the European starling: A follow-up study'.</p> <p>Revised version of September 4 2018.</p> <p>Contains one data file and one R script to reproduce the analyses in the paper.</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.